0000000000363950
AUTHOR
Samuel Jacquiod
Améliorer la croissance des plantes ?
Samuel Jacquiod et Manuel Blouin, du laboratoire Agroécologie, proposent une nouvelle approche basée sur la sélection des microbiotes rhizosphériques.La sélection végétale ou amélioration végétale est apparue il y a environ 10 000 ans, avec la domestication des céréales. Cette pratique, basée sur la reproduction sexuée des plantes, consiste à croiser entre eux des spécimens qui présentent des caractéristiques d’intérêts, qu’elles soient ornementales ou agronomiques (résistance aux maladies/insectes, meilleure production, qualités nutritionnelles ou gustatives). De génération en génération, les plantes descendantes sont sélectionnées jusqu’à obtention d’une nouvelle variété ayant fixée les c…
Artificial selection of root microbiota associated to plant phenotype changes
International audience; Artificial selection applied at community level is an important, but still growing topic in the field of ecology andexperimental evolution [1-3]. Its recent implementation to microbial communities holds not only appealingpromises in terms of fundamental knowledge about selection itself [3], but also in terms of relevant applicationsto our society, including bioremediation [4] and plant traits enhancement [5]. Here we transposed the conceptof artificial selection of communities to perform experimental evolution of root microbiota inducing relevantphenotypic changes in plants. We grew ten successive generations of four weeks old Brachypodiumdistachyon inoculated with a…
GENEFISHING: AN ALTERNATE METAGENOMIC APPROACH FOR CAPTURING TARGETED BACTERIAL DIVERSITY IN AN ENGINEERED RECIPIENT E. COLI STRAIN
International audience; The metagenomic approach, defined as the direct recovery and cloning of bacterial DNA from the environment in domesticated bacterial hosts has been widely used to study bacterial populations and their functional genes in numerous environments. The advantage of this approach over conventional culture based techniques is that it encompasses a wider range of bacteria by bypassing the bias of uncultivability of more than 99% of the bacteria in soil. However, in complex and rich environments such as soils, the huge level of bacterial diversity requires construction, handling and screening of several million clones in order to cover a significant proportion of bacterial ge…
Long-term organic and mineral fertilization strategies shape the rhizosphere microbiota and performance of lettuce
International audience; Belowground plant-microbe interactions are crucial for plant development and health. Although previous studies have shown that soil microbial communities are influenced by fertilization strategies, less is known about the aboveground plant response to the rhizosphere microbiota assemblage shaped by agricultural management strategies. In our study, we aimed to investigate the effects of long-term fertilization strategies across field sites on the rhizosphere prokaryotic (Bacteria and Archaea) community composition and plant performance. We conducted growth chamber experiments with lettuce (Lactuca sativa L.) cultivated in soils from two long-term field experiments sit…
Determinisms of plant and microbiome interactions : a multidisciplinary approach involving high-throughput phenotyping
International audience
Rhizosphere Bacterial Networks, but Not Diversity, Are Impacted by Pea-Wheat Intercropping
International audience; Plant-plant associations, notably cereal-legume intercropping, have been proposed in agroecology to better value resources and thus reduce the use of chemical inputs in agriculture. Wheat-pea intercropping allows to decreasing the use of nitrogen fertilization through ecological processes such as niche complementarity and facilitation. Rhizosphere microbial communities may account for these processes, since they play a major role in biogeochemical cycles and impact plant nutrition. Still, knowledge on the effect of intecropping on the rhizosphere microbiota remains scarce. Especially, it is an open question whether rhizosphere microbial communities in cereal-legume i…
Construction of simplified microbial consortia to degrade recalcitrant materials based on enrichment and dilution-to-extinction cultures
AbstractThe capacity of microbes degrading recalcitrant materials has been extensively explored from environmental remediation to industrial applications. Although significant achievements were obtained with single strains, focus is now going toward the use of microbial consortia because of advantages in terms of functional stability and efficiency. While consortia assembly attempts were made from several known single strains, another approach consists in obtaining consortia from complex environmental microbial communities in search for novel microbial species, genes and functions. However, assembling efficient microbial consortia from complex environmental communities is far from trivial d…
Impact of phosphate fertilization and arbuscular mycorrhiza on the development, nutrition and quality of micropropagated walnut rootstocks.
The English walnut (Juglans regia L.) is the main species cultivated for the production of edible nuts. Due to heterozygosis, the characteristics of agronomical interest of walnut cultivars are not inherited via seed propagation. In vitro plant tissue culture thus plays a key role in mass propagation of high-quality walnut rootstocks. Micropropagation of walnut explants needs an ex vitro acclimatization phase to repair the in vitro induced abnormalities, and further requires a post-acclimatization growth in greenhouse conditions when plantlets become photoautotrophic. However, poor survival and slow growth rates are common difficulties encountered in nurseries when establishing micropropaga…
Artificial selection of rhizosphere microbiota associated to phenotypical changes in plant functions
International audience; Artificial selection applied at community level is an important, but still growing topic at the interface of ecology and evolution. Its recent implementation to microbial communities holds appealing promises not only in terms of fundamental knowledge about selection itself and the levels at which it may be used, but also in terms of relevant applications to our societies, including bioremediation and agroecology. In this experimental evolution study, we performed an artificial selection of rhizosphere microbial communities inducing relevant phenotypic changes in plants. In total, we grew more than 2200 Brachypodium distachyon plants, consisting in ten consecutive gen…
Artificial selection of rhizosphere microbiota associated to phenotypical changes in plant functions
International audience
Evidence of a core microbiota shaped by plant and earthworm interactions across soils
Prod 2018-139a EA AGROSUP INRA BIOME IPM; International audience; While having distinct niches, plants and earthworms have occupied soils over geological times, mutually influencing each-others. These macroorganisms are considered “ecosystem engineers”, actively modifying soil physical structure, which notably provides specific habitats for microorganisms: the rhizosphere and the drilosphere (casts/burrows produced by earthworms). In this study, we aimed to disentangle the relative importance of both macroorganisms in shaping microbial community assembly in different soil types, and determine the extent and modalities of how rhizosphere and drilosphere communities may coalesce with each-oth…
Deciphering strategies of a river-sediment microbial community to cope with anthropogenic metal contamination
Metal contamination poses biotoxicity and bioaccumulation issues, affecting both abiotic conditions and biological activity in ecosystems. For a century, the MetalEurop foundry released zinc, copper, cadmium and lead directly into the river "la Deûle", resulting in a 30-fold increase in metal concentrations in downstream sediments compared to upstream. We used an integrative approach coupling in situ sequencing of both DNA and RNA, Horizontal Gene Transfer analysis (HGT), and microcosm monitoring in order to fully understand the mechanisms driving community adaptation to metal pollution. We applied the ecological concept of Functional Response Groups (FRGs) to decipher the adaptive toleranc…
Sélection artificielle de microbiote rhizosphériques associés à des changements phénotypiques de traits de plante
International audience; La sélection artificielle appliquée au niveau des communautés est un sujet grandissant à l’interface de l’écologie et de l’évolution. Son implémentation relativement récente à l’écologie microbienne s’avère prometteuse non seulement en termes de connaissance fondamentale sur le principe de sélection en luimême, mais aussi en termes de potentiel d’application, notamment en bioremédiation et en agroécologie.Nous avons utilisé l’évolution expérimentale afin de sélectionner artificiellement des communautés microbiennes rhyzosphériques induisant des changements phénotypiques chez leurs hôtes. Durant dix générations consécutives, nous avons fait pousser plusieurs lignées d…
Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production
A promising keratin-degrading strain from the genus Chryseobacterium (Chryseobacterium sp. KMC2) was investigated using comparative genomic tools against three publicly available reference genomes to reveal the keratinolytic potential for biosynthesis of valuable secondary metabolites. Genomic features and metabolic potential of four species were compared, showing genomic differences but similar functional categories. Eleven different secondary metabolite gene clusters of interest were mined from the four genomes successfully, including five common ones shared across all genomes. Among the common metabolites, we identified gene clusters involved in biosynthesis of flexirubin-type pigment, m…
A core microbiota of plant and earthworm interaction? Phylogenetic and functional aspects
International audience; The core microbiota concept has been proposed to describe the subset of a microbiota (e.g. the rhizosphere microbial community) associated with a given host (e.g. a plant) going beyond macroenvironment differences (e.g. soil type), and characterized by taxonomic markers (e.g. 16S rRNA gene sequences). Its existence has been questioned by geographical studies, showing the overruling soil type effect in shaping microbial communities. As far as biotic determinants are concerned, several “hosts” or macroorganisms are impacting a given habitat and its specific microbial community. In soils, there is an overlap between the so-called rhizosphere and the drilosphere, defined…
Beyond the piechart: 16S rRNA amplicon in microbial ecology studies
National audience